On two occasions the gauge on my 800GS indicated I had fuel but stalled. Re-starting even after fueling was difficult at best. Now, again, after fueling and with the gauge indicating fuel I am unable to get the bike started. I've had to charge the battery twice.

This exact thing has been discussed here *somewhere* recently - within the past 4-6 weeks or so. I don't remember what the solution was nor could I find the thread last night, but if you're willing to search a little, you'll find your answer. Sorry I can't be more helpful, but it's here. Somewhere.

How much gas is indicated when the bike stalls? Is this different than before? How long does your battery last when trying to restart?

The fuel pump is an on demand type and you should hear it spool up when the key is turned on. Does it? If truly out of gas it should take a little time and easily detected.

The battery should have a full charge to start. I would check the battery to ensure the clamps are clean and tight. Next check the voltage drop on the battery at rest and when cranking. Big drops in voltage indicate a bad cell. Original batteries were an issue.

The fuel pumps are in the tank for cooling. Habitually running the tank low, causes the pumps to overheat and shortens the life of one.

Bad fuel, letting the bike set long periods of time with ethanol fuel can result in a mixture that corrodes the fuel pump. The corrosion plugs filters and injectors.